Contacts of the strand formed by residues 290 - 294 (chain A) in PDB entry 1IR1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A HIS* 3.7 19.3 - - + +
158A GLU* 3.8 48.9 - - + +
161A LYS* 5.4 8.3 - - + +
162A LEU* 4.1 25.4 - - + -
199A PHE* 5.5 1.1 - - + -
263A PRO* 2.9 23.2 + - + +
264A ILE* 3.7 21.1 - - + -
265A VAL* 3.0 29.1 + - - +
288A GLY 4.0 1.8 + - - +
289A LEU* 1.3 74.9 - - - +
291A LEU* 1.3 59.3 + - - +
324A ASP* 3.3 17.9 - - + +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PRO* 4.4 7.4 - - + -
264A ILE* 4.7 1.3 - - - -
265A VAL* 3.5 16.2 - - + +
267A HIS* 4.1 4.9 - - + +
277A ASN* 4.7 3.4 - - - +
280A LEU* 3.9 25.4 - - + -
281A SER* 4.0 26.7 - - - +
284A CYS* 4.0 11.4 - - - -
290A LEU* 1.3 75.5 - - - +
292A HIS* 1.3 70.6 + - - +
293A ILE* 3.7 18.2 + - + -
322A GLY 3.7 21.8 - - - +
323A GLY* 3.8 2.4 - - - -
324A ASP* 2.8 45.2 + - - +
325A HIS* 3.3 4.0 + - - -
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Residues in contact with HIS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A KCX 3.9 7.4 - - - -
239A TYR* 3.3 40.7 - + + -
264A ILE* 4.0 7.7 - - + +
265A VAL 2.9 14.7 + - - +
266A MET* 3.1 14.3 - - + +
267A HIS 3.0 24.6 + - - -
290A LEU 4.2 0.4 - - - -
291A LEU* 1.3 71.4 - - - +
293A ILE* 1.3 68.7 + - - +
294A HIS* 4.3 1.7 + - - -
325A HIS* 3.0 36.0 + - + +
327A HIS* 2.8 42.2 + + - -
377A VAL* 3.8 16.2 - - + -
401A GLN* 4.0 3.1 - - - -
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Residues in contact with ILE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A HIS* 3.5 10.5 - - + +
269A TYR* 3.2 42.2 - - + -
277A ASN* 3.3 25.1 - - - +
291A LEU* 3.7 25.4 - - + -
292A HIS* 1.3 77.7 - - - +
294A HIS* 1.3 61.7 + - - +
318A LEU* 3.8 14.6 - - + -
322A GLY 4.2 1.8 - - - +
323A GLY* 3.8 20.2 - - - -
325A HIS 3.0 20.0 + - - +
326A ILE* 3.4 21.7 - - + +
327A HIS* 3.6 10.4 + - - -
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Residues in contact with HIS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A KCX 3.3 28.7 - - - -
204A GLU* 3.2 31.5 + - + +
266A MET* 4.0 10.3 - - + -
267A HIS 3.0 7.0 + - - +
268A ASP* 3.4 32.3 - - - +
269A TYR* 3.4 9.5 + - - -
270A LEU 4.7 0.2 + - - -
292A HIS* 4.0 2.3 + - - +
293A ILE* 1.3 73.3 - - - +
295A ARG* 1.3 60.2 + - - +
296A ALA* 2.9 42.4 + - + +
327A HIS* 3.7 16.6 - + - +
501A CAP 2.9 36.0 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il